Structural classification of HTH DNA-binding domains and protein–DNA interaction modes
R Wintjens, M Rooman - Journal of molecular biology, 1996 - Elsevier
This paper constitutes an attempt to rationalize the structural similarities and differences that
are observed among the HTH DNA-binding domains, and the various modes of protein – …
are observed among the HTH DNA-binding domains, and the various modes of protein – …
Artificial intelligence challenges for predicting the impact of mutations on protein stability
Stability is a key ingredient of protein fitness, and its modification through targeted mutations
has applications in various fields, such as protein engineering, drug design, and deleterious …
has applications in various fields, such as protein engineering, drug design, and deleterious …
Physical and molecular bases of protein thermal stability and cold adaptation
… with T m close to the living temperature (37C) to hyperthermostable proteins with T m of
more than 90C [7]. The heat denaturation temperature or melting temperature T m hot ≡ T m is …
more than 90C [7]. The heat denaturation temperature or melting temperature T m hot ≡ T m is …
[HTML][HTML] PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality
… where ΔΔG M, m is the experimentally measured folding free energy change of mutant m
and ΔΔG P, m its predicted value, obtained with eqs. (1)-(3). An iterative parameter reduction …
and ΔΔG P, m its predicted value, obtained with eqs. (1)-(3). An iterative parameter reduction …
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0
… To avoid any redundancy in our database, we considered only one value per mutant,
which is noted ΔΔG M and is defined as an average of all available measured ΔΔG values. …
which is noted ΔΔG M and is defined as an average of all available measured ΔΔG values. …
BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations
… In addition, the terms forumla and forumla were introduced to account for the possible
creation of packing defects: forumla , where forumla is the Heaviside function, and V w and V m …
creation of packing defects: forumla , where forumla is the Heaviside function, and V w and V m …
[HTML][HTML] Optimality of the genetic code with respect to protein stability and amino-acid frequencies
… element M(a,a'). We then symmetrize M by setting M(a,a') = [M(a,a')+M(a',a)]/2 and only
consider the lower half of M(a <a'). This procedure does not define the diagonal elements of …
consider the lower half of M(a <a'). This procedure does not define the diagonal elements of …
Contribution of cation-π interactions to the stability of protein-DNA complexes
… Column 4 indicates the localization of the cation-π pair in terms of the major (M) and minor
(m) … m and M refer to pairs observed at the minor and major groove sides, respectively. …
(m) … m and M refer to pairs observed at the minor and major groove sides, respectively. …
Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local …
… mutations are computed with the C m C w assumption or … proteins have the same backbone
structure (C m C w ). This … structures and to use the C m C w approximation, especially …
structure (C m C w ). This … structures and to use the C m C w approximation, especially …
PoPMuSiC, an algorithm for predicting protein mutant stability changes. Application to prion proteins
… where C m and C w are the mutant and wild-type conformations and S m and S w the mutant
and … The conformations C m and C w of the mutant and wild-type protein are assumed to be …
and … The conformations C m and C w of the mutant and wild-type protein are assumed to be …